LOCUS       NZ_CP043290             5847 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain WCHEC025985 plasmid p3_025985, complete
            sequence.
ACCESSION   NZ_CP043290
VERSION     NZ_CP043290.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN12158048
            Assembly: GCF_022559025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5847)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     The complete genome of Escherichia coli strain WCHEC025985
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5847)
  AUTHORS   Long,H., Feng,Y. and Zong,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-AUG-2019) Center of Infectious Diseases, West China
            Hospital, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan
            610041, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 200.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022559025.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:20:03
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,230
            CDSs (total)                      :: 5,108
            Genes (coding)                    :: 4,788
            CDSs (with protein)               :: 4,788
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 90
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 320
            CDSs (without protein)            :: 320
            Pseudo Genes (ambiguous residues) :: 0 of 320
            Pseudo Genes (frameshifted)       :: 97 of 320
            Pseudo Genes (incomplete)         :: 228 of 320
            Pseudo Genes (internal stop)      :: 47 of 320
            Pseudo Genes (multiple problems)  :: 48 of 320
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP043290.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5847
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="WCHEC025985"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="p3_025985"
                     /geo_loc_name="China: Chengdu, Sichuan"
                     /collection_date="2018-05"
     gene            complement(join(4948..5847,1..492))
                     /locus_tag="FYK42_RS25950"
                     /old_locus_tag="FYK42_26405"
     CDS             complement(join(4948..5847,1..492))
                     /locus_tag="FYK42_RS25950"
                     /old_locus_tag="FYK42_26405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001493761.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ISKra4-like element ISKpn19 family transposase"
                     /protein_id="WP_001493761.1"
                     /translation="MQLTLQIVITDESGSSRTEELMTIQKSGETRNDIGLSVSESKLLL
                     NTVQQSVVQLQADEYTQHHIRCPHCLAARRIKGKQKIRYRTLFGVIPVSGLRVYRCRCE
                     ESDTKTVSLLSDWAGDYSHPALKYIETRWASMISYEMTTRLLKDILPVGHSLNASTVRN
                     HLCQVAQRLDAEAEAHSGFLSGCPRDWGNLPRPGKPLVVGIDGGYVRDRDDKKRNFEII
                     AGKSFSVGAPADTRRFGFVQKDDCHPERRLMTHLSAQGMQANQQIFFLSDGADNLRDLQ
                     FGMYPESTHVLDWFHITMRLKVLMQYARGLLVSDPEAGSKVLALLESIKRYLWHGNVVA
                     ALEHIDNCVMYCDDPELSYPSLKSLQKHLDEMYTYIRNNKMMIPNYGEMRRYGEPVSTA
                     FVESTINEVIARRMAKKQQMQWSRKGAHYLLQTRTAVLNNELQDKFVCWYPGFQSDGKG
                     PAMAA"
                     /name="ISKra4-like element ISKpn19 family transposase"
     gene            complement(529..1101)
                     /locus_tag="FYK42_RS25955"
                     /old_locus_tag="FYK42_26410"
     CDS             complement(529..1101)
                     /locus_tag="FYK42_RS25955"
                     /old_locus_tag="FYK42_26410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001493762.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0000150 - DNA strand exchange activity [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase family protein"
                     /protein_id="WP_001493762.1"
                     /translation="MQYAYIRVSSADQNTARQEEALSKAGFQPDKICVEHASAKDTNRP
                     GLQELLGQLRPGDTLLVHSIDRLCRNMSDMCAVTTRLRDQGVTLIFLKEQLTFSAGTNN
                     PMQELQLHMMSAFSQFERALLKERQADGIAAKKARGEKTGRPGADIKKIQEIDALRSRG
                     VRLRIACDHAGLGVSTYYKLRHQMNNQ"
                     /name="recombinase family protein"
     gene            complement(1238..1783)
                     /locus_tag="FYK42_RS25960"
                     /old_locus_tag="FYK42_26415"
     CDS             complement(1238..1783)
                     /locus_tag="FYK42_RS25960"
                     /old_locus_tag="FYK42_26415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001493763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid pRiA4b ORF-3 family protein"
                     /protein_id="WP_001493763.1"
                     /translation="MVWRRLRIAADTSLAALHFIFQIVQGWGDDHLHQFHIYGKDYGIS
                     YEGGIGFVDNPFRVVIDDFAFDAGDRFTYEYNFFEHWLHDIRVEAIYENSTLKAPFCIS
                     GHGMPGATAADEFDKTLAFLEAIVNADDETTVGEIRPFADDLDAVRFNRHKINRQLSRL
                     DLASPVLEPEVIWLGRRR"
                     /name="plasmid pRiA4b ORF-3 family protein"
     gene            2350..2463
                     /locus_tag="FYK42_RS26260"
                     /old_locus_tag="FYK42_26425"
     CDS             2350..2463
                     /locus_tag="FYK42_RS26260"
                     /old_locus_tag="FYK42_26425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001517211.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHAKAPLAAATGN"
                     /name="hypothetical protein"
     gene            complement(4010..4666)
                     /locus_tag="FYK42_RS25965"
                     /old_locus_tag="FYK42_26435"
     CDS             complement(4010..4666)
                     /locus_tag="FYK42_RS25965"
                     /old_locus_tag="FYK42_26435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001516695.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="quinolone resistance pentapeptide repeat protein
                     QnrS1"
                     /protein_id="WP_001516695.1"
                     /translation="METYNHTYRHHNFSHKDLSDLTFTACTFIRSDFRRANLRDTTFVN
                     CKFIEQGDIEGCHFDVADLRDASFQQCQLAMANFSNANCYGIEFRACDLKGANFSRTNF
                     AHQVSNRMYFCSAFISGCNLSYANMERVCLEKCELFENRWIGTNLAGASLKESDLSRGV
                     FSEDVWGQFSLQGANLCHAELDGLDPRKVDTSGIKIAAWQQELILEALGIVVYPD"
                     /name="quinolone resistance pentapeptide repeat protein
                     QnrS1"
     ARG             complement(4014..4666)
                     /name="qnrS1"
                     /gene="qnrS1"
                     /gene_name="quinolone resistance pentapeptide repeat
                     protein QnrS1"
                     /tool="amrfinderplus"
                     /drug_class="QUINOLONE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          1976..2463
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.858"
                     /coverage="93.0"
                     /evalue="7.55e-176"
ORIGIN
        1 atgattcctc accgttgagg cattcaggct gtggcccacc ggcagaatat ctttcagcag
       61 acgagtcgtc atttcatagg agatcatcga ggcccagcgg gtttcaatat atttcagtgc
      121 cgggtgagaa taatcgccgg cccagtcgct gagcaaactg actgtctttg tatcactctc
      181 ttcacaacgg caccggtaca cccgaagccc ggataccgga ataacgccaa acagcgtccg
      241 gtaccgtatt ttctgtttgc ctttgattct gcgcgcagca aggcagtgag ggcaccggat
      301 atggtgttga gtatattcgt ctgcctgcag ctggaccacc gactgctgga ccgtattcag
      361 caacagcttg gattctgaca ccgataatcc gatgtcgttc cgggtctccc ctgatttctg
      421 gattgtcatc agttcctccg ttcgactgga gcctgattca tcggtgatga ctatctggag
      481 cgtcagttgc atcattgcct cctgctgtgg tggatgacta tctcccggct actggttgtt
      541 catctggtga cgaagcttat aatatgtgga aacgccaagg cccgcatggt cgcaggcgat
      601 cctgagcctg acccctctgc ttctgagtgc gtcaatttcc tggatctttt tgatatcggc
      661 gccggggcgc cctgtttttt caccccgtgc ttttttcgcg gcgatgccgt cggcctgcct
      721 ttccttcagt aaggctcgtt caaactggct gaatgccgac atcatgtgca gctgcagttc
      781 ctgcatcgga ttgtttgtgc cggcgctgaa cgtcagctgc tctttcagaa aaataagggt
      841 aacgccctgg tcacgaagcc gggtggtgac agcgcacata tccgacatat tccggcaaag
      901 gcgatcgatg gaatgaacca gaagcgtatc accagggcgt aattgcccca ggagttcctg
      961 taaccccggg cggtttgtgt ccttcgcgct ggcatgctca acacaaattt tatcaggctg
     1021 aaaacccgcc tttgacaatg cctcttcctg acgggccgta ttctgatcgg ccgagcttac
     1081 cctgatgtag gcatattgca cgcaaaacct ccggaaggtc tttaaacatc atagagattt
     1141 aaagaataat ccataaacac tgatttaggg aggtttatag acattttttc ggggatctga
     1201 gaggcatgct gaaaacgtat acctttatag acatcagtca gcgacgacgg cccagccaga
     1261 taacttcagg ctccagtacc ggagatgcaa ggtcgagcct gctcagttgc cggttgattt
     1321 tgtggcggtt gaacctgaca gcatccaggt cgtcagcaaa agggcggatc tcgccgaccg
     1381 ttgtttcatc atccgcatta acgatagctt caagaaacgc cagggtttta tcgaactcat
     1441 ccgcagctgt ggctccgggc ataccatggc cgcttataca aaacggcgct ttcagcgtag
     1501 agttttcata aatggcctca acacgaatgt catgaagcca gtgctcaaag aaattgtatt
     1561 cataggtaaa gcgatcgcca gcatcaaaag caaaatcatc aatcacgacc cggaacggat
     1621 tatcgacaaa accgatgcct ccttcgtagg agataccgta atctttgcca taaatgtgaa
     1681 attgatggag atggtcgtcc ccccagccct gcactatctg gaaaatgaag tgaagcgcgg
     1741 ccagtgacgt gtcggcagca attctcagcc gacgccagac catcggactg actccatgaa
     1801 ctgctatttt gatgacgtag atcttcatag tcagcaggta ttgttatgaa atgatggtgg
     1861 ttattttaac ccctgtagat ggcatcattc gatggctgcc ccgaggtttt tcatgctctc
     1921 ctggcaggtg aaaaatgtag ctgtagggcg taagtgaaaa atgcaggagt cgatgaaatt
     1981 acgcctcctc gctcactcgg tcgctacgct ccggacgtga gactgcggcg ggcgttaccg
     2041 gctcagaagt aaaggagtag gctagtagca atcaaattgg gaaaggaaga gaaaaggaag
     2101 cggcgttgcc gtttttccat aggctccgcc cccctgacaa gcatcacaaa atctgacgct
     2161 caaatcagtg gcggcgaaac ccgacaggac tataaagatc ccaggcgttt ccccctggta
     2221 gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt ccgctgttat
     2281 ggccgcgttt atctcattcc acgcctgaca ctcggttccg ggaaggcagt tcgctccaag
     2341 ctggactgta tgcacgaacc ccccgttcag tccgactgct gcgcctgttc cggtaactat
     2401 cgacttgagt ccaacccgga aagacatgca aaagcgccac tggcagcagc cactggtaat
     2461 tgatttagag gagttagtct tgaagttatg cgccggttaa ggctaaactg aaaggacaag
     2521 ttttggtgac tgtgctcctc caagccagtt acctcggttc aaagagttgg tagctcagag
     2581 aaccttcgaa aaaccgcctt gcagggcggt tttttctttt tcaagcgaaa gactacccgc
     2641 tgaattaaat aatctcaagt agcaacatga aatctaacga gtcagtgtcg agctagaaga
     2701 tggtgaggac agagtaatac ttgaattagt gcagctagat gattcaacgg tattaatcat
     2761 tctatcaagg cgaaccatac atttctcaac gacaagccca cctctaccat cactgctaat
     2821 gttggtcaca aatggacctg cttggcttga gcagccagca agaattactg atgacagaaa
     2881 aaccaatgag agaattacct ttttcataaa agccccagaa aatagagaag taggaataat
     2941 cttatctttt aatttgttaa tcaacataaa cgatatttac cataacatct cttgcccgca
     3001 ccgctgaaaa cgcctcagag ccattttgag gcgaacgggc cgtttccggc acctttccca
     3061 gcaccaaccc ctgaaaaacg cgcctgatga tttctgcgca tctgcatggc tatgcacgaa
     3121 catgcctggc cggaatttta gcggctaaaa tcctgcgaac tgctcaaaag gctcgctgaa
     3181 ccccatcgat aacggtgaac gggtgcacag tttactgtgc ggtcgtgagg cgttgagcaa
     3241 cgagctttgc gaggcggtag gggttctgag agccagctgc aggctcagga gaaaacattc
     3301 tgttttcggg gcagataccg caaatgacgt cattttgcgg cgtctgccct atcctgcatc
     3361 gcaacgtcta aaggatgtga gcacaaacgc cagcactttg cgaatcctgc cctcgatctg
     3421 aacaaaagca aaatttcgta cgtacgaaat tcagggtatc aggctgcgcc tgatgaaatg
     3481 tttttggtgc cggcggtact ccaaaaacac atcttgtccg acagttttgt ggtgccggcg
     3541 aagcggcggt ggccacaaaa catttcctgt ccccatcgat tcattcgaga aacataagag
     3601 gcgaagaagg ggtcagtttg gagatcggaa atttttgtac gttaagcgca ttatttaacc
     3661 aatcttggtt cgtaaggggt tgattttgcg tcagtggcta tcgcttttaa gttgtcgctc
     3721 ttgcagtatc gcatttaggt tatccgatta aggtcaaacc tctgaaaatg ccgtatagcg
     3781 cgggagtaca ccctattgct ataggtaagt ctgttcaaaa aacaggctta ccgtacaata
     3841 attctctata tccaaactga cccctaagtg acccactgct atatggctct attgtgaaga
     3901 cgcctgaggg taaaaattta tacatggttg tccctatgtc tattattgca aggttgacaa
     3961 tattattcgt tttataaatt tgagcgttta aaatcacaca tcaaagcaat tagtcaggat
     4021 aaacaacaat acccagtgct tcgagaatca gttcttgctg ccaggctgca attttgatac
     4081 ctgatgtatc gactttgcgg ggatctaaac cgtcgagttc ggcgtggcat aaattggcac
     4141 cctgtaggct aaattgcccc cagacatctt cggaaaaaac acctcgactt aagtctgact
     4201 ctttcagtga tgcacccgct aggttcgttc ctatccagcg attttcaaac aactcacatt
     4261 tttctaaaca aaccctctcc atattggcat aggaaagatt acatccagaa ataaatgctg
     4321 agcaaaagta catacgatta ctcacttgat gggcaaagtt tgttcgggaa aagttggcac
     4381 cttttaaatc acacgcacgg aactctatac cgtagcaatt ggcattactg aagtttgcca
     4441 tcgcaagttg gcattgttgg aaacttgcat cacgaagatc tgcgacatca aagtggcagc
     4501 cttcgatatc accctgttca atgaacttgc agttgacgaa tgtcgtatca cgcaagttag
     4561 cacgtcgaaa gtcgctgcga atgaatgtgc aagcggtgaa ggtgagatca cttaagtctt
     4621 tatgtgaaaa gttgtggtgc cgatatgtat gattgtaggt ttccatgagt actccttgtt
     4681 gaaaggaggg ctagactacc attatacata tgccaagaca ttaaaataaa agcctgttac
     4741 atcaacacat tacaacccct caatttacct gttttaagtg gtcaaattgg cgcgtagagc
     4801 gcctatcgct cttgcattgg cacgcggccc tgttgaaaaa agttattcgc tttagatagg
     4861 gttaggagag ccgtgcttcg ccggtaaaaa atcggactat ccgacgcagg gcggacgaga
     4921 gcataaaaaa tattggggca gcgtgagcta tgctgccatc gctggtccct tcccgtcact
     4981 ttgaaaaccc ggataccagc agacaaattt atcctgcagt tcgttattca aaacggcggt
     5041 ccgggtctgt aacaaataat gagccccttt tctgctccac tgcatctgct gctttttggc
     5101 cattcgtctg gcgatcactt cattgatcgt ggattccaca aacgcggttg ataccggctc
     5161 tccgtaccga cgcatttcgc cgtagtttgg gatcatcatc ttattattcc ggatgtaggt
     5221 atacatttca tccagatgtt tttgcaggga tttcaggcta ggatagctga gttcagggtc
     5281 atcgcaatac ataacgcaat tatcaatatg ttccagcgca gcgacaacat tgccatgcca
     5341 gagatatcgt ttaatgcttt ccagcagtgc cagaacttta ctccccgcct ctggatctga
     5401 taccagcagt ccccgggcat attgcatgag caccttcagc ctcatggtga tatgaaacca
     5461 gtccagcaca tgcgttgact cagggtacat accgaactgg aggtccctga gattatccgc
     5521 gccgtcggac agaaaaaata tctgctggtt ggcctgcatt ccctgcgctg aaaggtgggt
     5581 catgagcctg cgttccggat gacagtcatc cttctgaaca aaaccgaagc ggcgggtgtc
     5641 agcaggcgca ccaacggaaa aagacttccc ggcaataatt tcaaaattac gctttttgtc
     5701 atcccgatcg cgaacataac caccatctat acccaccaca agcggttttc ctggcctggg
     5761 caggttcccc cagtcgcggg ggcagccgga aagaaaacct gaatgagctt cagcctcagc
     5821 gtcaagacgc tgcgccacct ggcataa
//
